rs716873

Variant names:

• chr14-91580360-G-A
• rs716873
• ENST00000774285.1:n.74-44G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000774285.1(ENSG00000300830):​n.74-44G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 152,232 control chromosomes in the GnomAD database, including 1,496 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.13 (1496 hom., cov: 33)
• Consequence: ENSG00000300830 ENST00000774285.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.726
• Publications: 2 publications found

Genes affected

ENSG00000300830 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.172 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000774285.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000300830	ENST00000774285.1		n.74-44G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19782 AN: 152114 Hom.: 1496 Cov.: 33

Gnomad AFR AF: 0.0735

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.0312

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.223

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.144

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.130 AC: 19787 AN: 152232 Hom.: 1496 Cov.: 33 AF XY: 0.125 AC XY: 9306 AN XY: 74446

African (AFR) AF: 0.0736 AC: 3055 AN: 41536

American (AMR) AF: 0.115 AC: 1764 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.194 AC: 673 AN: 3470

East Asian (EAS) AF: 0.0311 AC: 161 AN: 5182

South Asian (SAS) AF: 0.108 AC: 522 AN: 4818

European-Finnish (FIN) AF: 0.117 AC: 1240 AN: 10594

Middle Eastern (MID) AF: 0.223 AC: 65 AN: 292

European-Non Finnish (NFE) AF: 0.174 AC: 11869 AN: 68018

Other (OTH) AF: 0.143 AC: 302 AN: 2114

Alfa AF: 0.151 Hom.: 269

Bravo AF: 0.126

Asia WGS AF: 0.0710 AC: 249 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.65
PhyloP100		-0.73

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs716873; hg19: chr14-92046704;